TY  - JOUR
A1  - Sheng, Gui-Lian
A1  - Basler, Nikolas
A1  - Ji, Xue-Ping
A1  - Paijmans, Johanna L. A.
A1  - Alberti, Federica
A1  - Preick, Michaela
A1  - Hartmann, Stefanie
A1  - Westbury, Michael V.
A1  - Yuan, Jun-Xia
A1  - Jablonski, Nina G.
A1  - Xenikoudakis, Georgios
A1  - Hou, Xin-Dong
A1  - Xiao, Bo
A1  - Liu, Jian-Hui
A1  - Hofreiter, Michael
A1  - Lai, Xu-Long
A1  - Barlow, Axel
T1  - Paleogenome reveals genetic contribution of extinct giant panda to extant populations
JF  - Current biology
N2  - Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an similar to 5,000-year-old giant panda from Jiangdongshan, Teng-chong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions.
Y1  - 2019
U6  - https://doi.org/10.1016/j.cub.2019.04.021
SN  - 0960-9822
SN  - 1879-0445
VL  - 29
IS  - 10
SP  - 1695
EP  - 1700
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Chen, Shun-Gang
A1  - Li, Ji
A1  - Zhang, Fan
A1  - Xiao, Bo
A1  - Hu, Jia-Ming
A1  - Cui, Yin-Qiu
A1  - Hofreiter, Michael
A1  - Hou, Xin-Dong
A1  - Sheng, Gui-Lian
A1  - Lai, Xu-Long
A1  - Yuan, Jun-Xia
T1  - Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China
JF  - Mitochondrial DNA Part A
N2  - Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
KW  - Camelus bactrianus
KW  - mitochondrial genome
KW  - ancient DNA
KW  - phylogeny
KW  - maternal lineages
Y1  - 2019
U6  - https://doi.org/10.1080/24701394.2019.1659250
SN  - 2470-1394
SN  - 2470-1408
VL  - 30
IS  - 7
SP  - 786
EP  - 793
PB  - Routledge, Taylor & Francis Group
CY  - Abingdon
ER  -